Small-pool polymerase chain reaction (PCR) constitutes the PCR amplification of a trinucleotide repeat in multiple small pools of input DNA containing in the order of from 0.5 to 200 genome equivalents. Products are resolved by agarose gel electrophoresis and detected by Southern blot hybridization under conditions that allow the identification of products derived from single-input molecules. The method allows the detailed quantification of the degree of repeat-length variation in a given sample, including the detection of common variants and those alleles present only in a small subset of cells. Detailed analysis of repeat dynamics is essential for a complete understanding of the molecular mechanisms that generate diversity and lead to disease in the unstable trinucleotide DNA repeat disorders.